[gmx-users] mpi problems: "topol.tpr made for 2 nodes .."

Soren Enemark blegbirk at yahoo.dk
Wed Jul 26 18:19:49 CEST 2006

Dear all,
 we are currently trying to set up Gromacs to run in parallel on a 3 dual-core machines with centOS ver. 4 .
 But we face the following error message when we try to run mdrun_mpi:
 Program mdrun_mpi, VERSION 3.3
 Source code file: init.c, line: 69
 Fatal error:
 run input file topol.tpr was made for 2 nodes,
              while mdrun_mpi expected it to be for 1 nodes.
 Can anybody help us with this?
 The error message came after running:
 grompp -f md.mdp -c b.gro -p topol.top -v -np 2
 followed by:
 mpirun -np 2 mdrun_mpi -s -v -np 2
 I should add, that it as we have lam/mpi installed and working, since a check as
 mpirun -np 2 ls
 does not give errors.
 Also lamboot -v seems to exit fine:
 [rasponi at bicluster TEST]$ lamboot -v
 LAM 7.0.6/MPI 2 C++/ROMIO - Indiana University
 n-1<5535> ssi:boot:base:linear: booting n0 (bicluster.bioing.polimi.it)
 n-1<5535> ssi:boot:base:linear: finished
 [rasponi at bicluster TEST]$
 Hope some of you guys out there can help us out.
 All the best,
 Soren Enemark
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